In an alternate 21st century, the robotics industry undergoes a period of rapid advancement worldwide. By the year 2050, Japan has firmly established itself as the leader in robotic technology and manufacture with Daiwa Heavy Industries. As the technology evolves to include robotic enhancements to the human body, the blurring of the line between man and machine triggers a sudden shift in world opinion. In response, the U.N. passes a unilateral ban of further research and development on robotics in 2067. Japan fiercely objects to this ban, but is unable to prevent its passage. In protest, Japan withdrew from international politics and chose to pursue a policy of high-tech national isolation. While only trade continues, Japan disappears from the world scene. Ten years later, a series of bizarre incidents lead the American technology police agency SWORD to believe that Japan has concealed extensive development of banned technologies through the use of the RACE network. SWORD dispatches a unit of special agents to infiltrate Japan and gather intelligence on the country. Vexille, a veteran agent among the group, uncovers the horrifying truth behind the ten years of isolation.

Futuristic post-war Japan is divided into four military regions, each led by conflicting nations trying to gain complete control over the country. While the Boundary War—fought with the help of humanoid mecha weapons called AMAIM—has long been over, the rivalry between these factions is still ongoing, and, as a result, the Japanese are heavily oppressed. Amou Shiiba, a 16-year-old orphan boy who is secretly rebuilding an abandoned AMAIM named Kenbu, stumbles upon Gai, an autonomous AI in need of battery power. By choosing to help one another, Amou and Gai find themselves at the center of a disaster, and Amou is labeled a terrorist and cast out of society. Even so, Amou refuses to remain idle in the face of injustice, and he embarks on a long journey rife with struggle and companionship. His aim transitions from leading a peaceful life to liberating the Japanese people.

The year is 2045, and artificial intelligence has undergone tremendous developments. Governments use them as weapons, engaging in never-ending warfare to sustain their economies. The mercenary group GHOST, headed by Major Motoko Kusanagi, is no stranger to this landscape. However, the rapid innovation of this technology causes a new threat to loom over the horizon. Having left Public Security Section 9, Kusanagi and her group are involved in many operations worldwide related to these proxy wars. But a seemingly simple job of locating an arms dealer drags GHOST into a hidden conflict against cybernetically enhanced individuals, who have inexplicably gained extreme intelligence and physical abilities. Dubbed post-humans, their emergence sets off a chain of events leading to the reunion of Section 9. Armed with a new mission, it is up to Kusanagi and her reestablished team to prevent global chaos at the hands of these post-humans.

Far from the city's noise lies Torishirojima—a quaint and peaceful island where time seems to move slowly. Hairi Takahara, a young boy nursing a wounded heart, uses the recent death of his grandmother as a quiet reason to leave the city for a summer retreat to Torishirojima. Upon reaching the island, Hairi finds himself surrounded by a refreshing, laid-back atmosphere, a far cry from the hustle and bustle he is used to. After moving in with his aunt, Kyouko Misaki, he prepares to spend the summer helping her sort through a shed full of artifacts his grandmother collected over the years alongside his cousin, Umi Katou, who is staying with them. While adjusting to the island's slower pace, Hairi decides to spend his free time exploring. He soon meets the cheerful Tsumugi Wenders; the antisocial Shiroha Naruse; the wandering Kamome Kushima; and the sharp-tongued Ao Sorakado. Drawn into their lives and the island's subtle mysteries, Hairi is gradually swept up in a summer filled with fun, nostalgia, and life-changing moments that will stay with him forever.